Table 1.
Existing promising and potential molecules against 3CLpro from SARS CoV-2
| S/No | PubChem CID | Binding free energy (kcal/mol) |
Tools used | Interacting residues | Refs |
|---|---|---|---|---|---|
| 1 | 5,7,3′,4′-Tetrahydroxy-2′-(3,3-dimethylallyl) isoflavone(11610052) | − 29.57 | Molecular operating environment (MOE) | Thr25, Thr26, Leu26, His41, Val42, Ser46, Met49, Tyr54, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192 | [42] |
| 2 | Cyanidin 3-glucoside(197081) | − 8.4 | Autodock Vina | Glu166, Asn142, His163, Gln189, Asp187, Thr26, Met49, Gly143, His164, Gln189, Cys145 | [43] |
| 3 | Baicalin(64982) | − 8.1 | Autodock Vina | Gly143, Leu141, Gln189, Met165, Asn142, Glu166, Pro168 | [43] |
| 4 | Glabridin(124052) | − 8.1 | Autodock Vina | Leu141, Glu166, Met49, His41, Met165 | [43] |
| 5 | Quercetin 3-vicianoside(44259139) | − 8.3 | Autodock Vina | His163, Glu166, Ser144, Leu114, Gly143, Thr26, Arg188, Asp187, Met165, His164, Gln189, His41, Thr25, Asn142, Phe140, Cys145 | [44] |
| 6 | Myricitrin(5281673) | − 8.9 | Autodock Vina | Tyr54, Asp187, Arg188, Leu141, Phe140, His172, Glu166, Ser144, His164, His163, Leu37, Asn142, Gly143, Thr26, Cys145, Met165, Met49, His41 | [45] |
| 7 | Oolonghomobisflavan-A(14520989) | − 75.5 | CDOCKER | Thr25, Asn142, His163, Glu166, Arg188, His164, Gly143, Met165, His41, Phe140, Leu141, His172, Ser144, Thr24, Cys145, Leu27, Met49, Asp187, Gln189, Gln192, Val186, Thr190, Pro168, Leu167 | [46] |
| 8 | Birinapant(49836020) | − 8.1 | Glide Schrodinger Suite | Thr25, Thr26, Leu26, His41, Val42, Ser46, Met49, Tyr54, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192 | [47] |
| 9 | Carfilzomib(11556711) | − 8.6 | Glide Schrodinger Suite | Cys145, His164, Glu166, Gln192, Asn142, Gln189, His41 | [48] |
| 10 | 6-Oxoisoiguesterin(21575473) | − 9.1 | Autodock Vina | Arg189, Met49, Met165, Cys145 | [49] |
| 11 | 22-Hydroxyhopan-3-one(21582894) | − 8.6 | Autodock Vina | Arg189, Met49, Met165, Cys145 | [49] |
| 12 | Crocin(5281233) | − 8.2 | Autodock 1.5.4 tools | Thr135, Asn133, Thr199, Lys137, Lys5, Phe3, Arg4, Arg131, Asp197 | [50] |
| 13 | Carnosol(442009) | − 8.2 | Autodock 1.5.6 tools | Cys145, His164, Glu166, Gln189, Met165, Arg188, Cys44, Met49, His41, Thr45, Thr25, Thr26, Leu27, Gly143, Ser46, Asn142 | [51] |
| 14 | Rosmanol(13966122) | − 7.9 | Autodock 1.5.6 tools | Cys145, Gly143, Thr25, His41, Met49, Asn142, His143, Glu166, Leu141, Ser144, Met165, Phe140 | [51] |
| 15 | Withanone(21679027) | − 4.4 | Glide Schrodinger Suite | Thr24, Thr25, Thr26, Leu27, His41, Met49, Tyr54, Asn142, Gly143, His164, Met165, Glu166, Arg188, Asp188, Gln189, Cys145 | [52] |
| 16 | Nelfinavir(64143) | − 7 | Autodock Vina | His163, Gln189 | [53] |
| 17 | CMPD23B | − 118.6 | Igemdock | Arg40, Tyr54, Cys85, Phe181, Arg188, Arg40, Tyr54, Glu55, Met82, Asn84 | [54] |
| 18 | Amodiaquine(2165) | − 7.4 | Glide Schrodinger Suite | Leu141, ARG187, Glu166, His41 | [55] |
| 19 | Remdesivir(121304016) | − 7.9 | Glide Schrodinger Suite | Gln191, Ala192, Thr190, Gln189, Arg188, Asp187, Leu141, Asn142, Gly143, Ser144, Cys145, His164, Met165, Glu166, Leu167, Pro168, Thr26, Leu27, Met49, Tyr54, His41 | [56] |
| 20 | Ribavirin(37542) | 2 | Glide Schrodinger Suite | Leu4, Gln189, Met49, Val3, Ser46, Cys145, Thr25, Thr24, Thr45 | [57] |
| 21 | Telbivudine(159269) | 2 | Glide Schrodinger Suite | Thr190, Leu50, Glu47, Ser46, Met49, Val3, Gln189 | [57] |
| 22 | Lopinavir(92727) | − 10.8 | MMPBSA.py module of AMBER16 | Met49, Met165, Pro168, Gln189, His41, Ala46, Met49, Glu166, Leu167, Leu187, Gln189, Ala191, Ala193 | [58] |
| 23 | Ritonavir(392622) | − 14.9 | MMPBSA.py module of AMBER16 | Leu27, His41, Met49, Phe140, Asn142, Gly143, His164, Met165, Glu166, Asn142, Gly143, Ser144, Cys145, Met165, Glu166, Asp187, Gln189 | [58] |
| 24 | Saquinavir(441243) | − 9.8 | Glide Schrodinger Suite | His41, Cys44, Tyr54, Met49, His172, Glu166, Met165, His164, His163, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, Thr25, Thr26, Leu27, Asp187, Arg188, Gln189, Thr190, Ala191 | [56] |
| 25 | Simeprevir(24873435) | − 10 | Autodock Vina | Glu166, Met165, Gln189, Phe140, Cys145, Asn142, Leu27, His41, Ser46 | [59] |
| 26 | Paritaprevir(45110509) | − 9.8 | PyRx v0.8(Autodock Vina) | Ser46, Met49, Leu50, Cys145, Pro168, Thr24, Thr25, Leu27, His41, Cys44, Thr45, Glu47, Phe140, Gly143, Glu166, Gln189 | [60] |
| 27 | Hypericin(3663) | − 10.7 | CDOCKER | Gly143, Glu166, Asn142, Glu166, His41, Cys145, Asn142, Glu166, Gln189, Met165 | [43] |
| 28 | Eravacycline(54726192) | − 8.8 | Glide Schrodinger Suite | Met49, Gln189, Tyr190, Gln192, Glu166, Met165, Asn142 | [48] |
| 29 | Valrubicin(454216) | − 9.2 | Glide Schrodinger Suite | His41, His164, Asn142, Met165, Glu166, Gln189 | [48] |
| 30 | Viomycin(135398671) | − 77.2 | CDOCKER | Glu166, Phe140, Asn142, His164, Ser144, Gly143, His41, Met49, Met145, Gln189, Arg188, Asp187, His163, Cys145 | [61] |
| 31 | Elbasvir(71661251) | − 9.9 | Glide Schrodinger Suite | Thr25, Thr26, His41, Met49, Met165, Gln189, Thr190. | [48] |
| 32 | Fluvastatin(446155) | − 7.7 | Autodock Vina | Glu166, His163. | [62] |
| 33 | Methisazone(667492) | − 6.8 | Glide Schrodinger Suite | His41, His49, Tyr54, Cys145, Met165, Gln166, Leu167, Pro168, Asp187, Arg188, Gln189, Thr190, Gln192. | [63] |